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revision 1.519 by heimbach, Thu Jul 28 14:35:47 2005 UTC revision 1.886 by jmc, Mon Oct 1 19:30:47 2007 UTC
# Line 4  $Name$ Line 4  $Name$
4      Notes on tags used in MITgcmUV      Notes on tags used in MITgcmUV
5      ==============================      ==============================
6    
7  o adding precip control xx_precip  o change units of EmPmR (inside the code) from m/s to kg/m2/s (mass flux) but
8  o moved ptracer ctrl index 17 -> 32    leave input file unchanged. Affects results @ truncation level (cg2d match)
9      and update output of experiments: lab_sea(6), global_ocean.90x40x15(10),
10      global_ocean.cs32x15(11x3,10), natl_box(11), tutorial_global_oce_latlon(11)
11      + adjoint results: global_ocean_ebm(11) and lab_sea (12).
12      Next: will retire convertEmP2rUnit (simply using mass2rUnit instead).
13    
14    checkpoint59h
15    o pkg/exf:
16      - improve vectorization by moving if-statement out of loops in
17        exf_mapfields, exf_radiation
18      - exf_bulkformulae.F: introduce 2D fields and vectorize code
19    o pkg/kpp: added the salt plume scheme (ALLOW_SALT_PLUME) to KPP package
20    o testreport:
21      - allow to test for Qnet & SeaIce monitor output; clean-up ALLOW_BULK_OFFLINE
22        monitor & update offline_exf_seaice exp. output.
23      - AD testing: pass/FAIL according to Grad. output accuracy (instead of Cost)
24    o pkg/seaice:
25      - bug fix in the evp solver: boundary conditions were affected be
26        masking of zMax/zMin (changes results)
27      - minor bug fix in boundary conditions in seaice_calc_strainrates
28        (changes results for no_slip)
29      - seaice_lsr.F: make interpolation of eta dependent on boundaries
30      - replace hardcoded lower limit for zeta (zMin) by runtime parameter
31      - add a test to lab_sea, that tests the Hibler and Bryan (1987) ocean
32        stress formulation and no-slip boundary conditions
33    o pkg/ptracers: Temporary fix for PTRACERS_useGMRedi & PTRACERS_useKPP
34      in gad_calc_rhs.F ; add few safety stops in initialisation phase.
35    o pkg/seaice: a first HSALT time stepping equation has been checked in
36    o pkg/seaice: replaced maskW with seaiceMaskU and maskS with seaiceMaskV
37      in seaice_lsr.F; this solves the pkg/seaice-pkg/obcs problem
38      without requiring DO-IF statements
39    o pkg/thsice:
40      use continuous power-law function for partition of energy between lateral
41      melting/freezing and thinning/thickening ; old code using step function
42      still available with #undef THSICE_FRACEN_POWERLAW
43      update output of exp: aim.5l_cs.thSI, global_ocean.cs32x15.icedyn & .thsice
44    o testreport: change AD testing : check against results/output_adm.txt
45      using same scripts as for forward test.
46    
47    checkpoint59g
48    o adjoint testing: in preparation for changing testreport:
49      - output format: cost and grad written on separated lines
50      - ad output results in directory "results" (instead of "results_ad")
51    o pkg/seaice: adding ice salinity HSALT as a prognostic variable
52    o pkg/seaice: changes for using pkg/seaice with pkg/obcs
53    o pkg/ecco: allow user defined cost function contributions
54    o testreport:
55      Allow to choose (per experiment) the list of tested output variables
56       and the main variable (used to issue a pass/FAIL ) ;
57      - for now, done by adding the specific list in file: [exp]/input/tr_checklist
58      - default is unchanged: >cg2d< , (T,S,U,V,5 tracers)_[min,max,mean,StD] ;
59      Also modify printing of summary:
60       a) ">" NN "<" indicates the "main" variable (used for pass/FAIL)
61       b) echo the list of tested variables in the individual summary.txt of
62          each experiment.
63    o new S/R GLOBAL_SUM_TILE to compute global sum independently of number of
64      threads and number of processes (with #define GLOBAL_SUM_SEND_RECV)
65      (but still depend on the tile decompostion of the domain).
66    o pkg/seaice: change a discretization detail to make the B-grid code
67      "more symmetric". This change is likely to remove all "ridges/leads" that
68      where quasi-aligned with the grid in B-grid solutions. It may also be
69      the solution to the stress coupling issues with the B-grid.
70    o each tested exp: add a "run" directory with a standard ".cvsignore" file ;
71      remove .cvsignore from input dir. (since testreport no longer run here).
72    o pkg/thsice:
73     - cleaning: move common block out of "THSICE_2DYN.h" (removed) to "THSICE_VARS.h"
74     - fix reshaping of sea-ice just after advection:
75       melt all the ice only if ice-volume is too small.
76     - re-visit lateral/thinning repartition of melting (modifs from May 04, 2007):
77       prevent lateral melting if sea-ice fraction is too close to iceMaskMin ;
78     and update experiment global_ocean.cs32x15.icedyn (+start from pickup files).
79    o external_forcing_surf : extend the use of salt_EvPrRn & temp_EvPrRn (fresh-water
80      tracer content) to linFS or no RealFreshWaterFlux ; default remains unchanged.
81    o define mass2rUnit & rUnit2mass as units conversion factor, used for surface
82      forcing. mass2rUnit: from mass per unit area [kg/m2] to r-coordinate unit
83      (z-coord: =1/rhoConst ; p-coord: =gravity) ; rUnit2mass is just the reverse;
84      and remove horiVertRatio (& recip_horiVertRatio). Affects truncation error
85      of exp. global_oce_in_p: 10 16 16 14 16 13 16 16 16 13 13 13 16 13 13 12 16
86      -> update output.txt
87    o pkg/cd_code: add brackets in multiple terms sum (S/R CD_CODE_SCHEME):
88     this affects truncation error: -> update output.txt of exp:
89      global_ocean.90x40x15 (fw&adm), lab_sea (fw&adm) & lab_sea.lsr,
90      ideal_2D_oce, isomip.htd, natl_box, tutorial_global_oce_latlon.
91    
92    checkpoint59f
93    o pkg/autodiff: zero_adj resets an ajoint variable to zero (in adjoint mode)
94    o pkg/ctrl: ctrl_bound  forces parameter corrections to stay in
95      a bounded range (in forward mode)
96    o pkg/ecco, ctrl, autodiff and mom_common:
97     internal parameter controls, completements of implementations
98    o add few EXCH S/R (UV_BGRID, UV_DGRID, SM) for B & D-Grid velocity & 2nd Moment Sxy.
99    o use UV_BGRID exch for dxV,dyU: for now, only with pkg/exch2 & forward ;
100      (not seem any difference in testing results).
101    o pkg/cd_code: use the right EXCH calls (for CS-grid); but problem remains
102       at face corners.
103    o pkg/generic_advdiff:
104     - in GAD.h, define as parameters (iMinAdvR,iMaxAdvR,jMinAdvR,jMaxAdvR)
105      loop range indices for computing vertical advection tendency
106      and do the calculation in the interior only (no overlap) ;
107      for now, only implemented for SOM advection (to save CPU time).
108     - add argument "withSigns" to S/R FILL_CS_CORNER_TR_RL (needed for SOM_xy moment)
109    o exch2 adjoint
110      First set of changes:
111      - add exch2 hand-written adjoint templates
112      - exch2 hand-written no longer use TAF-flag 'nownew_arg'
113        This will require cleanup in pkg/autodiff/*.F
114        (changed routines currently kept separate in verif. code/)
115      - Comment all relevant #ifndef ALLOW_AUTODIFF_TAMC
116        that used to hide exch2 or cubed-sphere specific code
117        (commented via 'cph-exch2')
118    o pkg/seaice
119      - Close southern and western boundaries for UICE/VICE when useOBCS=.TRUE.
120    o pkg/bulk_force: fix loading into Qsw of Short-Wave flux; and update
121       output of global_ocean.cs32x15.thsice .
122    
123    checkpoint59e
124    o exch2: new S/R that only use the cube-tracer (center-position) exchange:
125      for B-grid vector (not yet tested) and C-grid vector (<- only used
126      when option W2_USE_R1_ONLY in W2_OPTIONS.h is defined).
127    o starting implementation of Duffy et al. (GRL 1999) salt plume scheme
128      (#ifdef ALLOW_SALT_PLUME)
129    o gather_2d/scatter_2d: removed halo regions
130    o gmredi: add option (GM_taper_scheme='fm07') for Ferrari & McWilliams 2007
131      scheme and the corresponding test case (under front_relax dir). For now,
132      only available with Skew-flux form and not yet tested in realistic set-up.
133      adjoint: store directives updated, but gradient checks deteriorated,
134      so maybe GM/Redi adjoint is now broken.
135    o seaice adjoint
136      * add AREA, HEFF, HSNOW as control variable
137        (should not change lab_sea results)
138      * CTRL_OPTIONS.h needs new flag: CTRL_SET_OLD_MAXCVARS_40
139    o pkg/seaice:
140      * added computation of saltFlux in seaice_growth;
141        For time being, sea ice salinity is assumed constant
142        contribution of snow flooding to freshening of sea ice is neglected.
143        SEAICE_salinity is set in SEAICE_PARM01 of data.seaice and it
144        defaults to 0.0 in order to maintain backward compatibility.
145        Typical values for SEAICE_salinity are 4 to 10 g/kg.
146      * replaced dRf(1) with dRf(kSurface)*hFacC(kSurface) in seaice_growth.F
147      * added SEAICE_availHeatFrac, which specifies fraction of surface level
148        heat content used to melt or grow ice
149      * commented out cap of HICE: it helps keep ice thinner
150      * reintroduced cap of HEFF via MAX_HEFF and SEAICE_CAP_HEFF option
151      * applied OBCS T/S mask to HEFFM sea ice mask
152    
153    checkpoint59d
154    o standard name: {PKG}_DIAGNOSTICS_STATE to fill diagnostics array
155     for {PKG} state variables, and called from DO_STATEVARS_DIAGS.
156     (keep {PKG}_DIAGNOSTICS_FILL for non-state variables diagnostics)
157    o pkg/gmredi (gmredi_readparms.F): add some missing "_d 0"
158     and change default value of parameter "GM_Small_Number";
159     update output of exp: lab_sea (x2), cfc_example, global_ocean.90x40x15,
160       global_ocean.cs32x15 (x4), global_ocean_ebm, global_with_exf,  
161       tutorial_global_oce_biogeo, tutorial_global_oce_latlon
162    o pkg/ecco: cost function when applying pkg/smooth to controls
163    o pkg/ctrl: add forcingPrecond run time parameter
164    o pkg/seaice:
165     - replace ZMIN=4.e8 with ZMIN=0. in dynsolver.F as in C-grid code
166     - fix bug in metric terms of u-equation in LSR solver (implicit part),
167       changes verification/lab_sea
168     - rearrange implicit part of u-equation in LSR solver to make it easier to
169       read, understand, and debug. This causes changes at the truncation level.
170     - fix (serious) bug in the boundary conditions (sign error in the implicit
171       part) of the LSR solver. Changes all LSR results.
172     - fixed problem with HSNOW initialization to avoid thick snow when AREA
173       is initilized with small values - does not change lab_sea results.
174     - added HsnowFile initialization capability
175    o pkg/smooth: addition to model/src and pkg/ctrl so allow
176     initialization of pkg/smooth and application to control vector
177    o pkg/seaice: fix another bug in the LSR no-slip boundary conditons
178    o dependencies: pkg/profiles requires pkg/cal
179    o pkg/profiles:
180     - added option ALLOW_PROFILES_GENERICGRID
181         -> pkg/profiles can thus be used with any grid (e.g. cs32x15) assuming
182         that interpolation information (grid points and coefficients) is provided
183         within the netcdf input files.
184         -> sample matlab scripts can be found in MITgcm_contrib/gael
185         that allow you to prepare netcdf input files.
186     - also modified: cleaner include statements, cleaner error print statements,
187       cleaner stops when error, and more tests of the netcdf input files consistency.
188    o additional test (in global_ocean.cs32x15) using seaice+thsice pkgs.
189    o pkg/seaice:
190     - move seaice-diagnostics from seaice_do_diags to do_statevars_diags; this
191       requires a new routine: seaice_diagnostics_fill.F
192     - make sure that seaice does not move if not forced (pressure replacement
193       method, Hibler and Ip, 1995), changes results
194     - and new damping criterion for EVP solver according to Hunke, JCP, 2001
195     - SEAICE_evpDampC = > 0. turns it on (615. is the recommended value).
196       It is turned off by default (=-1.), because it changes the results.
197     - make it possible to read AREA from a file, too.
198    
199    checkpoint59c
200    o add S/R and diagnostics for oceanic mixed-layer depth
201    o move GMRedi call after all vertical mixing schemes (including KPP)
202    o pkg/thsice:
203     - ensure iceMask > iceMaskMin : this problem appeared after May-04 modifs
204      (melt only laterally if thin ice): update output of global_ocean.cs32x15.thsice
205    o pkg/obcs:
206     - bug fix for balance code
207    o pkg/seaice:
208      - allow values of SEAICE_elasticParm > 1
209      - add new parameter SEAICE_evpTauRelax as an alternative
210        to SEAICE_elasticParm
211      - make lsr boundary conditions free slip (by default), changes result
212      - add code for no slip boundary conditions for lsr
213      - set minimum of zeta to zero (and not 4e8) (changes results)
214      - add a cap on AREA after advecting AREA if seaice_growth is not called
215    o change calculation of Visbeck K:
216      - no longer depend on tapering scheme; instead, compute slope (limited
217        by GM_maxSlope). this is equivalent to what was comuted before with
218        clipping or linear tappering.
219      - fix vertical averaging (wrong by 1/2 level)
220      - leave the old version (but will not be maintained) within
221        #ifdef OLD_VISBECK_CALC / #endif
222      - update output of exp. ideal_2D_oce
223    o change error catch in calc_r_star to improve vectorization
224    o exf runoff and seaice: remove ALLOW_SEAICE from exf pkg files and
225      add #define ALLOW_RUNOFF in SEAICE_OPTIONS.h (when not using exf).
226    o adjoint:
227      Re-organized adjoint checkpointing according to Matt Mazloff
228      (but with modifs/completions/cleanups)
229      Storing is now bundled into large arrays to optimized I/O
230      (and second step in cleanup of the_main_loop)
231    
232    checkpoint59b
233    o coupler (pkg/atm_ocn_coupler, pkg/ocn_compon_interf, pkg/atm2d):
234      - export/import (between ocean & coupler) fields needed for ocean DIC.
235    o pkg/seaice:
236      - get rid of three more exchanges seaice_calc_viscosities (required
237        different loop boundaries in seaice_lsr and seaice_ocean_stress)
238      - bug fix in seaice_ocean_stress (update of lab_sea required)
239      - reduce loop boundaries to necessary minimum also in seaice_evp
240      - go back to the old way of computing deltaC/Z as the adjoint likes that
241        better
242    o Refresh of tutorial_global_oce_latlon (includes changing salinity-like
243      passive tracer to an Age Tracer) + update output.txt
244    o pkg/exf:
245      - implement A-grid / C-grid selection for wind-stress input files.
246      - clean-up exf_wind.F (remove us, use wspeed instead ; add wStress)
247      for now, in exf_bulk_largeyeager04.F only :
248      - change implementation for case where windspeed + 2. components wind-stress
249        are read-in. AND use rhoConstFresh to convert evap.
250    o pkg/seaice:
251      - use correct EXCH_UV for wind-forcing (on A-grid).
252      - change SEAICE_OPTIONS.h to limit the number of option combinations (regarding
253        SEAICE_EXTERNAL_FORCING & SEAICE_EXTERNAL_FLUXES); add corresponding stops.
254    o pkg/exf:
255      - default EXF options are now set in EXF_OPTIONS.h (ifndef ALLOW_AUTODIFF_TAMC)
256      EXF_INTERPOLATION:
257      - merge global_with_exf/code version of exf_interp_read.F
258        to the main code ;
259      - Add new option: EXF_INTERP_USE_DYNALLOC to use Dynamical Allocation when
260        reading the file ; Important: This options needs to be defined to recover
261        previous code.
262        otherwise, use fixed size array to read in (size=exf_interp_bufferSize).
263      - no longer loose real*8 precision along the way when using exf_iprec=64.
264    o pkg/seaice: rearrangement of common blocks (really needs more cleaning up)
265      - change discretisation of evp-solver in order to avoid another exchange
266        (changes lab_sea) and clean up a little
267      - replace SQRT(MAX(deltaC,SEAICE_EPS)) by MAX(SQRT(deltaC),SEAICE_EPS)
268        help the adjoint (this also changes the results slightly)
269      - add a few "_d 0" where they had been missing in seaice_evp.F
270      - cleaning up: remove unused seaice_calc_rhs.F
271    o pkg/exf: some cleaning-up:
272      - change various "constants" into runtime parameters
273      - cleaned-up Large&Yeager04 routine which should eventually
274        replace exf_bulkformulae.F (changed names of S/R and CPP)
275        and merged various ALLOW_ATM_WIND options
276     only used with thsice pkg (in thsice_get_exf.F):
277      - implement fixed turbulent transfert Coeff over ice (as in Large&Yeager04)
278        which are used when useStabilityFct_overIce=TRUE (= the default)
279      - change default values of ice & snow emissivity and scale downward LW
280        by ice & snow emissivity.
281    o pkg/thsice:
282     fix few little problems, in thsice_calc_thickn.F:
283      - growth vertically (and not laterally) if iceFrac == iceMaskMax
284      - melt only laterally if hIce < hThinIce (as the comments say)
285      and in thsice_extend.F:
286      - allow to form ice even when iceFrac == iceMaskMax (by increasing thickness)
287      - start to form ice as soon as the minimum ice-volume is reachable.
288     update output of test-exp: aim.5l_cs(thSI), global_ocean.cs32x15(thsice),
289      and cpl_aim+ocn
290    o pkg/kpp
291     - move computation of surface related input fields to KPP into a new
292       subroutine kpp_forcing_surf.F
293     - remove wrong (within bi,bj loops) EXCH calls.
294     - little cleaning (add argument myThid in last position, cvs header ...)
295     - for now, fix conservation problem by exchanging KPPviscAz (may not
296       be the best fix)
297    o pkg/seaice
298     - check for inconsistent evp parameter/cpp-flag combination
299     - remove leftover errIO flat for obsolete name list error handling
300    o OpenAD
301     - changed verification/OpenAD to full baroclinic setup (including GM/Redi)
302    
303    checkpoint59a
304    o pkg/seaice: some parameter clarifications and a little bit of clean up
305    o pkg/thsice: rename run-time parameters:
306       himin       -> hIceMin
307       himin0      -> hThinIce
308       hihig       -> hThickIce
309       i0          -> i0swFrac
310       transCoef   -> bMeltCoef
311       frac_energy -> fracMelting
312      add new parameters: hNewIceMax, fracFreezing, dhSnowLin
313       with default values (for now) that do not change the results.
314      remove old version of thsice vars advection in pkg/seaice.
315    o in FFIELDS.h:
316      - replace #ifndef ALLOW_EXF  by #ifndef EXCLUDE_FFIELDS_LOAD
317      - make pLoad & sIceLoad always available (but still only used if
318         ATMOSPHERIC_LOADING is #define).
319    o pkg/kpp: replaced _KPP_RL with _RL
320    o bug fixes for vertical diffusivity computations when both KPP and
321        3D diffusivity arrays are used; pkg/kpp/kpp_calc_diff_s & _t.F
322        are no longer updating the vertical diffusivity array
323        (passed as argument) but are (re-) setting those arrays.
324    o pkg/seaice: fix bug in evp solver, while doing that
325      - change (improve?) discretization of stress computations for both
326        cgrid-lsr and evp solver
327      - add a new routine to compute strain rates
328      - the above changes lab_sea results
329      - add no slip conditions for evp solver (off by default), lsr-version
330        may follow
331      - fix exchange for shear at Z-points (does not change lab_sea)
332      - retire SEAICEuseEVP, instead turn on EVP by setting SEAICE_deltaTevp
333        (to force the user to pick a time step since there is not "safe" way
334        of choosing it)
335      - add principal stress diagnostics
336      - rearrange fields for evp a little to avoid having to call a: too many
337        exchanges and b: exchanges for stress trensor components which we do
338        not have.
339      - modify Hibler+Bryan (1987) stress coupling so that it reuses information
340        of evp, complete rewrite for lsr case (latter is does not yet work
341        in all cases)
342    o pkg/kpp: add code to have mixing in shelf ice caverns
343      - add myThid to all kpp routines (long overdue)
344    
345    checkpoint59
346    o pkg/exf:
347      - fix wind-stress location: defined on A-grid (if ALLOW_ATM_WIND &
348        ALLOW_BULKFORMULAE or USE_EXF_INTERPOLATION), otherwise, defined on C-grid
349      - move exf header files from lower_case.h to UPPER_CASE.h ;
350        add missing cvs Header & Name
351      - add adjoint routines and flow dirs for newly used exch_uv_agrid routines
352      - add namelist param. selectStressGridPosition, exf_monFreq
353      - retire many _CLIM routines, and remove data.exf_clim
354        + params moved to data.exf
355        + climsst, climsss now handled by exf_set_gen, i.e.
356          climss?period=0 refers to constant field,
357          climss?period=-12 to monthly forcing
358      - split up namelists in data.exf
359    o pkg/seaice:
360      - remove seaice_exch and seaice_exch_uv
361      - remove superfluous exchange of theta
362      - add myThid to seaice_budget_ocean/ice
363      - add new interface for atmospheric wind forcing (C-grid only)
364        + new routine
365        + two new field (taux, tauy for stress over ice)
366        + removed one global field (DAIRN) for C-grid case only
367    o pkg/thsise
368      - 2nd set of modifs for thsice adjoint in conjunction with exf
369    o enable runtime flag useEXF (useCAL is set to .T. if useEXF=.T.)
370    
371    checkpoint58y_post
372    o Added capability for latitudinal dependence of Bryan and Lewis, 1979
373      vertical diffusivity, similar to that in MOM4; turned on using
374      #define ALLOW_BL79_LAT_VARY in CPP_OPTIONS.h and specified using
375      diffKrBL79*, diffKrBLEQ*, and BL79LatVary in runtime data file.
376    o Added capability for 3D specification of background vertical diffusion
377      coefficient.  This is done by (i) #define ALLOW_3D_DIFFKR
378      in CPP_OPTIONS.h and (ii) specifying file diffKrFile in runtime
379      "data" file that contains the 3D vertical diffusivity coefficients.
380    o ice dynamics (pkg/seaice) with thsice thermodynamics:
381      - add code within pkg thsice to advect & diffuse sea-ice fields
382      similar to (and will replace) what has been added in  seaice_advdiff.F,
383      but: - conserving Mass, Heat & Salt.
384           - better when using non-linear advection scheme (not yet fully tested)
385           - can also be used in atmospheric set-up (for now, only the diffusion).
386    
387    checkpoint58x_post
388    o IO option for global-file compact format:
389      - add options when generating topology (utils/exch2/matlab-topology-generator)
390      - add I/O capability (pkg/mdsio).
391      - adapt utils/matlab/rdmds.m to read this format.
392      for now long-line format not yet supported by pkg/mdsio (& exch2).
393    o shelfice: add a few diagnostics
394    
395    checkpoint58w_post
396    o p-coord. non-hydrostatic using reference profile for w <-> omega conversion:
397      rVel2wUnit & wUnit2rVel are computed from reference profile Tref,Sref
398      (and replace horiVertRatio in NH code).
399      Update output of exp.: tutorial_global_oce_in_p (useNHMTerms !)
400                         and tutorial_plume_on_slope (sensitive to truncation)
401    o seaice: if ALLOW_ATM_WIND is undefined use wind stress
402      directly to drive seaice model (C-grid only)
403    o exf: when input wind-stress (#undef ALLOW_ATM_WIND):
404     - reintroduce computation of wind from stress,
405     - compute tau (in exf_bulkformulae.F) from windstress averaged to
406       mass points to avoid tau = 0
407     - fix serious bug: (1/3) in Fortran is not the same as (1./3.)
408    o rdmnc.m: make it work with "global" files created with gluemnc
409    o rdmnc.m : some improvements in dealing with singleton dimension
410      (tested on all testreport mnc output files).
411    o genmake2: disable pkg/profiles if netcdf test fails.
412    o cpl_aim+ocn exp.: use consistent rhoConstFresh in Atm & Ocn; update output.
413    o move call to cal_readparms up to make calendar parameters/variable available
414      to all packages
415    
416    checkpoint58v_post
417    o change EOS (from POLY3 to JMD95P) in global_ocean.90x45x15 to get
418      useDynP_inEos_Zc tested.
419    o pkg/exf: changes to properly interpolate/mask/scale initial fields
420    o utils/matlab/cs_grid/read_cs: routines to speed up reading of CS510 fields
421      and portions thereof.  See read_cs.txt for description and examples.
422    o utils/matlab/cs_grid/bk_line: to compute transport through passages,
423      add a script (grt_circ_bkl.m) to generate broken-line between 2 points,
424      following the great-circle arc between those 2 points.
425    o trap un-initialized variable with pathscale compiler on weddell.mit.edu
426      (thanks to Constantinos): fix few problems and get (almost) all exp to pass.
427    o 2nd-Order Moment Advection Scheme (Prather, 1986): first check-in
428     - enable by setting #define GAD_ALLOW_SOM_ADVECT (in GAD_OPTIONS.h)
429     - used without limiter (AdvScheme=80) or with Prather limiter (AdvScheme=81)
430     - still needs work (not working with some options ; efficiency to improve)
431       and serious testing.
432     - use this scheme for temperature & salinity in 2 advection test exp.:
433       advect_xy & advect_xz, respectively.
434    
435    checkpoint58u_post
436    o new test-exp: fizhi-cs-32x32x40 (40 levels) to replace the 10 levels.
437    o move call to INI_FORCING from PACKAGES_INIT_VARIABLES to INITIALISE_VARIA.
438    o testreport: add option "-skipdir" to skip some test.
439    o exf: when input wind-stress (#undef ALLOW_ATM_WIND), by-pass turbulent
440      momentum calculation.
441    o gad_advection: fix vertAdvecScheme (if different from advectionScheme)
442    o some cleaning: usePickupBeforeC35 no longer supported ; remove this option.
443      remove checkpoint.F and the_correction_step.F (no longer used);
444      do the k loop inside CYCLE_TRACER (supposed to be more efficient).
445    o add option (linFSConserveTr) to correct for tracer source/sink due to
446      Linear Free surface
447    o pkg/seaice: fix a bug in the flooding algorithm: turn off the snow machine
448    o pkg/thsice: fix reading mnc-pickups
449    
450    checkpoint58t_post
451    o pkg/diagnostics: fix multi-threaded output (when singleCpuIO=F)
452    o pkg/mdsio:
453     - clean-up mdsio_readfield.F & mdsio_writefield_new.F and
454       move to new files: mdsio_read_field.F (S/R MDS_READ_FIELD) &
455       mdsio_write_field.F (S/R MDS_WRITE_FIELD);
456     - fix multi-threaded singleCpuIO option in MDS_WRITE_FIELD
457     - collect old S/R  in one file: mdsio_rw_field.F (now just a call to
458       either MDS_READ_FIELD or MDS_WRITE_FIELD )
459     - new S/R (to replace MDSWRITEMETA), which allows to write more
460       informations (variable names, time ...) to meta files.
461     - modify rdmds.m to give back the meta file content.
462    o pkg/diagnostics: change vertical interpolation to be safer, and more
463       flexible (define p-levels to interpolate to in data.diagnostics);
464      add argument to S/R DIAGNOSTICS_GET_POINTERS to catch the right
465       diagnostic pointer.
466    o pkg/seaice: more cleaning up of seaice_growth, added many comments
467    o pkg/exf: put runoff0 and runoff1 into the appropriate common block
468    o fix multi-category seaice:
469     - change cpp flag SEAICE_MULTILEVEL to more meaningful name:
470       SEAICE_MULTICATEGORY
471     - fix short wave heat flux
472    o pkg/seaice: change default (SEAICE_OPTIONS.h): use C-grid dynamics
473       and allow to use EVP solver. Change forward lab_sea: test both EVP
474       solver and LSR solver, and use C-grid dynamics (like lab_sea adjoint)
475    o Initial check-in of lab_sea adjoint
476      (very similar to natl_box_adjoint/code_seaice)
477      * used C-grid and EVP solver
478      * used KPP, GM/Redi
479      * uses inAdExact=.TRUE.
480      * gradient checks fail for both ADM and TLM
481        due to sensitive snow melt code in seaice_grwoth (look for "JZ")
482        f.d. gradients actually seem more problematic than ADM, TLM gradients;
483        issue is related to forward mismatch between g77 an ifort
484    o pkg/seaice: overhaul of thermodynamics
485     - growth.F and groatb.F are replaced by new routine seaice_growth.F
486     - budget.F is replaced by two new routines seaice_budget_ocean/ice.F
487     - move a few global fields out of SEAICE.h into seaice_growth.F and
488       make them 2D (FICE/QNETO/ ...)
489     - remove FO (it is the same as QNETO)
490     - introduce a few local fields to avoid modifying external fields such
491       as atemp, etc.
492    
493    checkpoint58s_post
494    o pkg/exf: moved exf_init_runoff.F to exf_init.F and exf_set_gen.F
495      changed exf_set_gen.F so that
496        genperiod=0 means input file is one time-constant field and
497        genperiod=-12 means input file contains 12 monthly means
498    o CG2D: use pre-computed solver main-diagonal (stored in common block);
499      this affects truncation error ; generate new output file for exp. which
500      fails: exp4(12d), fizhi-cs-aqualev20(12d), front_relax(10d),
501        global_ocean.90x40x15(10d), global_ocean.cs32x15(10d).thsice(11d).viscA4(10d),
502        ideal_2D_oce(10d), internal_wave(09d), isomip.htd(11d), matrix_example(07d),
503        MLAdjust(4x11d,12d), natl_box(11d), rotating_tank(12d),
504        tutorial_global_oce_in_p(10d), tutorial_plume_on_slope(11d),
505        vermix(12d).ggl90(12d).my82(11d).opps(12d).pp81(11d)
506    o start implementation of deep-atmosphere and anelastic formulation
507    o verification: remove 2nd copy of input files and use script "prepare_run"
508      to make a symbolic link to the 1rst copy (reduce downloaded size by ~81.M)
509    o mom_common/vecinv/fluxform: fix a few initialisation isssues
510    o profiles: fix for multithreaded case
511    
512    o diagnostics: rename few diags:
513      s/'PRESSURE'/'RCENTER '/g
514      s/'TICE    '/'oceFreez'/g
515      s/'TAUX    '/'oceTAUX '/g
516      s/'TAUY    '/'oceTAUY '/g
517      s/'SWFLUX  '/'oceQsw  '/g
518      s/DIFx/DFxE/g
519      s/DIFy/DFyE/g
520      and add few ocean-forcing diagnostics:
521      atmPload, sIceLoad, oceQnet, oceFWflx, oceSflux, surForcT & surForcS
522    o modifications to pkg/seaice/growth.F and budget.F, which change results of
523      lab_sea experiment: HSNOW was sometimes treated as effective and sometimes
524      as actual snow thickness.  It now refers everywhere to effective snow
525      thickness, meaning that for non-zero AREA, actual thickness is HEFF/AREA.
526    
527    checkpoint58r_post
528    o modifications to pkg/seaice/growth.F, which change results of
529      lab_sea experiment: fixes pertain to melting snow over open water, to
530      masking EVAP under sea ice, and to using the correct AREA variable for
531      computations of EVAP, PRECIP, HSNOW, and GHEFF
532    o add ability to read bathy, salt, and theta using MNC (off by def)
533    o add flooding algorithm and advection of HSNOW for pkg/seaice;
534      both are turned off by default and do no change any results
535    o seaice advection with pkg/thsice: a step toward the use of non-linear
536      advection scheme, but #ifdef or commented out for now (requires more EXCH).
537    o use standard version of PTRACERS_INI_VARIA in tutorial_tracer_adjsens
538      (identical results) and the standard version of EXTERNAL_FIELDS_LOAD
539      in natl_box (affects results @ truncation level: update output.txt)
540    o multi-threading and IO:
541      - replace some call to MDSIO S/R by the corresponding READ/WRITE_FLD S/R.
542      - remove most of BEGIN_MASTER/ END_MASTER around READ/WRITE_FLD S/R calls
543        (needed to work with SingleCpuIO): tested in all verif. exp.
544    o GAD: use simpler DST3 formulation as default (old version left within #ifdef)
545      affects the results (but none of the verification test uses this scheme).
546    o Adding some pkg/diagnostics capability to pkg/seaice
547      (will certainly be subject to changes)
548    o ctrl: adding new control variables:
549      lwflux, lwdown, evap, snowprecip, apressure, runoff
550    
551    checkpoint58q_post
552    o added CPP_EEOPTIONS.h flag DISABLE_MPI_READY_TO_RECEIVE.  Speeds up
553      1/6-deg Southern Ocean configuration by 8% on IBM Datastar and
554      high_res_cube configuration by 4% on Columbia.
555    o clean-up multi-threaded problems (reported by debugger tcheck on ACES);
556      add (in global_with_exf/code) a version of EXF_INTERP_READ without
557      dynamical allocation (seems to work in multi-threaded).
558    o new function "MASTER_CPU_IO" (=T if master thread & master CPU, if using
559      single CPU io) so that TAF does not have to see EESUPPORT.h
560    o pkg/seaice: implement sea-ice loading (when using RealFreshWaterFlux)
561    
562    checkpoint58p_post
563    o obcs: stop if obcs is used with useCDscheme = .true.
564    o shelfice:
565     - fix a sign error so that no slip at shelfice interface works
566     - remove stop for combination non-hydrostatic code and shelfice. That does
567       not mean, that the results are correct, but at least they are numerically
568       stable
569    o diagnoctics: modify UVELPHI and VVELPHI to include hfac (i.e. mass-weighted)
570    o added adjoint exch routined for all exch*3d* routines
571      and updated flow directives
572    
573    checkpoint58o_post
574    o replace calls to EXCH_Z & EXCH_UV_AGRID: use the new _3D_ version ;
575      remove old subroutines (_XY_ & _XYZ_); update the adjoint version.
576    o change controling S/R for writing pickup file (new S/R do_write_pickup)
577      and clean-up reading/writing of pickup files.
578    o fix local version of read/write pickup (NH part) in rotating_tank/code
579    o simplify EXCH interface:
580     - change _XYZ_ interface to _3D_ subroutine (with 3rd dim in argument list)
581     - not often used EXCH S/R (exch_z, exch_uv_agrid): keep only the _3D_ version
582    o added the regrid package
583    o shelfice:
584     - add a simple boundary layer scheme to reduce noise
585     - fix the indexing in shelfice_u/v_drag so that there will be actually drag
586    
587    checkpoint58n_post
588    o fix globalArea multi-threaded calculation: need to apply GLOBAL_SUM to
589       local variable (not in common block).
590    o lot of small changes for multi-threaded. Most tests (using OMP & ifort) pass.
591      - still problems with pkgs: mnc, exp2, dic, cal, exf (and probably more);
592      - still BEGIN_MASTER/END_MASTER to remove around READ/WRITE_FLD S/R calls
593        to work with SingleCpuIO.
594    o add "_d 0" to real constant of pkg/cfc subroutines ;
595       update exp. cfc_exemple & tutorial_cfc_offline output files.
596    o multi-threading and IO:
597      - all threads call READ_FLD S/R (needed if using SingleCpuIO):
598        (no BEGIN_MASTER/ END_MASTER around the call, but inside MDSIO S/R.
599      - barrier before and after reading.
600      - stop if other than master is calling MDS_WRITELOCAL (if #undef IO_THREAD_SAFE)
601      - avoid using MDS_WRITELOCAL for LAND pkg output.
602      - new S/R AIM_WRITE_PHYS (replaces AIM_WRITE_LOCAL) to write AIM physics
603        common-block variables ; Allows multi-threading with master-thread IO.
604    o change default MAX_NO_THREADS from 32 to 4 ;
605      and stop cleanly when MAX_NO_THREADS is too small.
606    o add S/R BAR_CHECK to check multi-threaded barrier synchronization
607    
608    checkpoint58m_post
609    o add a Non-Hydroatatic test (with 3-D Coriolis, NHMTerms, biharmonic Visc.
610       and side-drag) on CS-grid : global_ocean.cs32x15.viscA4
611    o make "tutorial_global_oce_latlon" from standard "global_ocean.90x40x15" exp.
612       keep global_ocean.90x40x15 (for AD testing) with former secondary test
613       (".qshyd") as the main test (mv output.qshyd.txt to output.txt)
614    o CVS modules: update MITgcm_verif_basic; remove MITgcm_verif_ocean & _verif_atmos;
615        add MITgcm_tutorials (= code + all the tutorials)
616    o ecco, option to compute cost for total ssh (mean+anom)
617    o consistent with addition of ptracer and ssh in pkg/profiles
618    o profiles: adding ptracer and ssh
619    o testreport: change multi-test output-file name
620      (from output.txt.{name} to output.{name}.txt)
621    o profiles: now ok for mutli-tiles case
622    o seaice: add 4 parameters for different advection schemes for area,
623      (effective) seaice thickness, enthalphy, and snow height. Their default
624      is the standard parameter SEAICEadvScheme
625    o calc_gw:
626     - add cosFacU in zonal viscous flux (harmonic.visc.).
627     - put back side-drag (call new S/R MOM_W_SIDEDRAG) and output.txt.
628       of tutorial_plume_on_slope.
629    o obcs_calc.F : fix index Pb in OBSeta & OBNeta (Thanks to Gianmaria).
630    o calc_gw: true flux-form, account for horizontal grid spacing.
631      update rotating_tank results, but not plume_on_slope (affected at
632      truncation level, 11 digits).
633    
634    checkpoint58l_post
635    o calc_gw:
636     - take bi,bj loops outside calc_gw to fix Pb with local array KappaRU,V
637     - remove side-drag for now (need to fix it); update plume_on_slope results.
638     - fix for partial-cell & non-uniform dz; update plume_on_slope results.
639    o commit code to make SST/SSS weights spatially variable
640      (based on either variable in-situ or variable initial T/S weights)
641    o pkg/ecco:
642      * commit code to relax deviations of xx_theta, xx_salt to 5*sigma,
643        now based on horizontally varying weights wthetaLev, wsaltLev
644      * cost_averagesflags now returns year indices in addition to day, month
645      * sflux balance is performed on annual basis
646        (sflxumm, sfluxmm2, bal_sfluxmm)
647      * for SSH anomaly, separate more cleanly contrib from T/P, ERS, GFO,
648        including separate counting and multipliers
649    o pkg/rbcs
650      * add all necessary infrastructure for pkg/rbcs levN adjoint checkpointing
651    
652    checkpoint58k_post
653    o testreport:
654     - always build in dir. "build" (if not there, mkdir build instead of building
655       & running in input)
656     - run in dir run (if it exists), in build otherwise.
657     - call prepare_run (if input/prepare_run exists)
658     - run multi-threaded test (with new option: "-mth") if file input/eedata.mth exists.
659    o pkg/exf modifications to interpolation and rotation routines for more
660       reasonable treatment of North Pole singularity: for tracers North Pole
661       value is set to northernmost zonal-mean value, for zonal velocity it is
662       set to zero, and for meridional velocity it is set to northernmost value.
663    o pkg/exf/exf_check_range.F
664     - add tile index to diagnostics and move stop statement to the very
665       end of the routine.
666    o pkg/diagnostics: (diagnostics_main_init.F)
667      define title of isomorphic variables according to the current config.
668    o pkg/thsice with pkg/seaice dynamics:
669    - fix domain of computation (interior only, required for exf) and do exchanges
670    - seaice-dynamics forcing: add atmospheric and seaice loading to SSH gradient
671    o towards a standard way of dealing with multi-threading in MONITOR
672      and ${PKG}_MONITOR (all except ptracers_monitor) subroutines.
673    o Pass variable viscosities (vertical and horizontal, e.g., KPP or Leith)
674       to W momentum equation in nonhydrostatic and quasihydrostatic runs.  
675    o make exf_monitor & seaice_monitor independant of the main (dynamics) monitor.
676    o pkg/seaice: fix SEAICEuseEVPpickup parameter (put it in a commom block)
677    o generic_advdiff: DST advection S/R : use local copy of velocity to compute CFL
678       (problems ? with gradient check in bottom_ctrl_5x5 adjoint test)
679    o tracer advection:
680     - clean-up and simplify calc_common_factors.F
681     - make a local copy of velocity and pass it (as u,v,r_Trans) to DST tracer
682       advection subroutine (but still not used within DST advection S/R)
683    o rename pkg aim_ocn_coupler to atm_ocn_coupler (later on, will be used without aim)
684    
685    checkpoint58j_post
686    o new driver S/R: LOAD_FIELDS_DRIVER to load external forcing fields
687      from file (collects calls previously in FORWARD_STEP)
688    o move call to SEAICE_MODEL from FORWARD_STEP to DO_OCEANIC_PHYS
689    o adjoint store dir. adjusted accordingly
690    o genmake2
691      replace target "ad_taf" by $(EXE_AD) ; add $(EXE_AD) to the make CLEAN list.
692    
693    checkpoint58i_post
694    o pkg/seaice: add parameter that allows to scale/turn off effect of seaice
695      on wind stress (SEAICEstressFactor defaults to 1.)
696    o Total number of Timers is finite (<=40): comment out 2 non-essential one
697      in the_main_loop.F to avoid Pb (e.g., when running fizhi test)
698    o vector_invariant: fix highOrderVorticity(=4.th.Order) advection
699      on CS-grid: no longer loosing mass.
700    o exf & curvilinear-grid: no longer modify longitude xC & xG.
701    o pkg/ggl90: fix sloppy output and fix a bug
702    o pkg/seaice: added SEAICEuseEVPpickup parameter
703      - Set to false in order to start EVP solver with
704        non-EVP pickup files when using SEAICEuseEVP
705      - fix sign error in diffusion in seaice_calc_rhs
706    
707    checkpoint58h_post
708    * Modifications for bottom topography control
709      o replace hFacC by _hFacC at various places
710      o replace ALLOW_HFACC_CONTROL by ALLOW_DEPTH_CONTROL
711      o add non-self-adjoint cg2d_nsa
712      o update autodiff support routines
713      o re-initialise hfac after ctrl_depth_ini
714      o works for 5x5 box, doesnt work for global_ocean.90x40x15
715    * Adding verification for 5x5 box (4-layer) bottom topography control
716    
717    checkpoint58g_post
718    o pkg/diagnostics: implement "periodic averaging diagnostics" (e.g.,
719       used for mean seasonal cycle, mean diurnal cycle); add an example
720       in verification/global_ocean.cs32x15/input.thsice/data.diagnostics
721    o pkg/ggl90:
722      - add parameter (minimum surface kinetic energy)
723      - fix bug (avoiding division by zero)
724    o couple pkg/thsice to pkg/seaice:
725      - modify advection in seaice to accomodate new scalar fields to be advected
726      - only muliDimAdection scheme work with seaice/thsice
727      - mapping of thsice-variables to seaice-variables, back and forth
728      - does not break the verification experiments, but does not give the
729        desired results either
730    o pkg/seaice
731      - make (default) second order advection a bit less confusing?
732    
733    checkpoint58f_post
734    o couple pkg/thsice and pkg/exf (as a preparation for coupling pkg/thsice
735      to pkg/seaice):
736      - new routines thsice_map_exf and thsice_get_exf provide the interface
737      - add an additional formal parameter to thsice_solve4temp
738    o pkg/exf:
739      - add new fields wspeed, snowprecip (to be able to couple to thsice)
740      - correct Stefan-Boltzmann constant
741      - new parameter for longwave surface emittance
742      - separate some stuff from exf_bulkformulae into new routines  
743        exf_radiation, exf_wind
744      - add new parameters and constants: longwave emissivity for ocean, ice
745        and snow, evaporation parameters over ice
746      - decouple wind/stress computation from ALLOW_BULKFORMULA: always compute
747        either wind from stress or stress from wind
748    o pkg/thSIce:
749    - split thsice_step_fwd.F in 2 S/R: thsice_step_temp.F & thsice_step_fwd.F
750    - put i,j loops inside S/R: THSICE_ALBEDO, THSICE_SOLVE4TEMP, THSICE_EXTEND
751       and THSICE_CALC_THICKN
752    - for now, call to THSICE_GET_BULKF remains inside i,j loops.
753    - add CPP option: ALLOW_DBUG_THSICE and header file THSICE_DEBUG.h
754      to make debugging easier.
755    - affects results (@ truncation level) of global_ocean.cs32x15.thsice: update output
756    o pkg/bulk_force:
757      - clean-up comments and parameters ;
758      - add new Bulk-Formulae from Large and Yeager, 2004, NCAR/TN-460+STR ;
759    o fix bug in aim+thsice albedo: snow & ice thickness arguments were switched;
760      generate new output for test-experiment: aim.5l_cs.thSI
761    o results_ad : rename "output.txt_adm" to "output_adm.txt" and change
762      testreport accordingly
763    
764    checkpoint58e_post
765    o SEAICE_CGRID adjoint done
766    o R_STAR adjoint implemented.
767      * Seems to just work (based on global_ocean.90x40x15/code_ad_nlfs/ )
768      * need to sort out init. of h0facc, etc.
769    o Make pkg/profile fully independent of ecco,cost, etc. stuff
770      to be able to use it in pure forward.
771    
772    checkpoint58d_post
773    o upgrade simple test-experiment to tutorial example:
774     step.1: duplicate the experiment and (step.2) will remove the old copy.
775      tutorial_barotropic_gyre      <- copy of exp0     (R1:barotropic_gyre_in_a_box)
776      tutorial_baroclinic_gyre      <- copy of exp1     (R1:baroclinic_gyre_on_a_sphere)
777      tutorial_global_oce_latlon    <- empty for now    (R1:global_ocean_circulation)
778      tutorial_global_oce_biogeo    <- copy of dic_example
779      tutorial_deep_convection      <- almost like exp5 (R1:nonhydrostatic_deep_convection)
780      tutorial_plume_on_slope       <- copy of plume_on_slope
781      tutorial_tracer_adjsens       <- copy of carbon   (R1:tracer_adjoint_sensitivity)
782      tutorial_global_oce_optim     <- empty for now (David ?)
783      tutorial_global_oce_in_p      <- copy of global_ocean_pressure
784     some tutorials (R1) were already checked-in under tutorial_examples in release1_branch
785    o correct a sign problem in cost_scat.F
786    o obcs and ptracers: fix boundary conditions for advections schemes
787      with larger stencil
788    o thsice adjoint: start
789    o mom_vecinv: add ISOTROPIC_COS_SCALING flags to mom_vi_hdissip for
790      completeness
791    o mom_fluxform: fixing the mutual use of ISOTROPIC_COS_SCALING
792      and COSINEMETH_III, add comments in default CPP_OPTIONS.h
793    o ptracers adjoint:
794      * avoid extensive recomputatations
795      * fix missing re-init. of gptr (missed by TAF)
796    o obcs: add a flag (OBCSprintDiags, defaults is true) that allows
797      me to turn off the excessive output to STDOUT that this package produces
798    o move NH metric terms & 3.D Coriolis S/R to pkg/mom_common
799      and add those terms in Vector-Invariant formulation.
800    o in ctrl pkg, if ALLOW_CAL, use monthly mean controls
801      if the control period (xx_hfluxperiod etc) is 0
802    o in profiles pkg, clean routines and fix details
803    o in ecco pkg, reading ssh data:
804      fix problem in case the model does not start at iter0=0
805    o fix mnc-pickup/restart for ptracers
806    o new package prifiles:
807      code to compute profile-based cost by Gael Forget
808      (modifs in ecco, ctrl, autodiff)
809    o Benign bug fix in initialization (spotted by M. Mazloff) of
810      ctrl_set_globfld_xz.F ctrl_set_globfld_yz.F
811    
812    checkpoint58c_post
813    o adjoint: finish NLFS adjoint and provide reference output in
814      verification/global_ocean.90x40x15/results_ad_nlfs
815    o seaice: add an EVP solver following Hunke and Dukowicz (1997) and the
816      documentation of CICE. Turn on by defining SEAICE_ALLOW_EVP in
817      SEAICE_OPTIONS.h and SEAICEuseEVP=.true. in data.seaice. Works only
818      with SEAICE_CGRID defined.
819    o move calendarDumps from "data" to "data.cal" and clean-up the code
820      with a simple call to pkg/cal S/R: CAL_TIME2WRITE
821    o add useEXF & useCAL flags (for now, set in hard-coded way)
822    o add S/R to compute NH-metrics terms & Coriolis f' in vertical momentum
823      (were missing in NH mode, and wrong in quasihydrostatic mode).
824      waiting for Chris updated version of calc_gw to add those CALLs.
825    o fix bug in quasihydrostatic S/R ;
826      add a test for this option: global_ocean.90x40x15.qshyd
827    o new S/R "SET_PARMS": set parameters that might depend on the use of some pkgs.
828      (called from INITIALISE_FIXED, after INI_PARMS & PACKAGES_READPARAMS)
829    o add on/off flag useOffLine for package OFFLINE
830    o seaice:
831      - modify advection so that it works also on the C-grid
832      - extend loop ranges in seaice_lsr and seaice_dynsolver; fixes
833        problem in multi-tile runs with C-grid
834      - add flags for clipping ice velocities and/or masking solver forcing
835      - fix drag (ocean on ice) formulation and a bug that caused noise in the
836        C-grid solver
837      - added a few comments to seaice_diffusion.F
838      - separate C-grid and B-grid versions more cleanly (UVM and seaiceMaskU/V
839        are now exclusive)
840      - add a new ocean-ice stress coupling method (Hibler and Bryan, 1987) which
841        required re-ordering the code a little:
842       + make DAIRN global variable (defined in SEAICE)
843       + move computation of the viscosities eta and zeta into a new separate
844         routine (because I need to recompute them in seaice_ocean_stress.F)
845    
846    checkpoint58b_post
847    o AIM+thSIce: fix sign of Short-Wave through the Ice ;
848      update output.txt of exp. aim.5l_cs.thSI
849    o various mnc cleanups and improvements:
850      + shrink lookup tables by factor of ~4
851      + better error reporting when running out of lookup space
852      + able to handle longer path/file names (up to 500 chars)
853    o adjoint:
854      - Another overhaul of store dirs. for NLFS to eliminate  "hidden" recomputations.
855      - TBD: "hidden" mom_vecinv recomp. in dynamics
856    o change forcing_In_AB to affects both T,S forcing and Momentum forcing
857     (allow to differentiate between forcing components using new integer flags:
858      momForcingOutAB=1/0 & tracForcingOutAB=1/0)
859     and add new flag to put Dissipation tendency out of Adams-Bashforth.
860    o ecco
861      - enable trend removal from SSH anomaly obs.
862    o adjoint
863      - a fix for PmEpR when #undef EXACT_CONSERV
864      - fix of "hidden" recomp. in thermodynamics (no TAF warnings)
865      - try to fix "hidden" recomp. in forward_step for NLFS
866        (NLFS seems broken sometimes after I checked it in)
867    o seaice:
868     - add c-grid version of the dynamic solver:
869       + three new routines that are the c-grid substitute lsr, dynsolver
870         and ostres
871       + put a few fields that were local to dynsolver into global common
872         blocks, so that I can move the computation of stresses etc into
873         seaice_lsr (saves coding but may break the adjoint).
874     - replace more hardwired parameters by runtime parameters
875     - add ice masks that mask the rhs of the implicit solvers where there
876       is no ice (commented out in seaice_dynsolver, because i am not sure
877       if this works properly), eventually this should replace the clipping
878       of ice velocities in seaice_dynsolver to +/-40cm/s.
879    o remove the BUILD_INFO.h include from CPP_EEOPTIONS.h and explicitly
880      include it only where its needed
881    o move balancing of fluxes before the call of external_forcing_surf
882    o seaice:
883      - correct units of turning angles (now they are really in degrees)
884      - move computation of GWATX/Y out of main routine into dynsolver
885      - initialize GWATX/Y in seaice_init
886    o Apply mask on Fresh-Water flux (needed for SSH forcing).
887      update output.txt of exp. global_ocean_ebm & cpl_aim+ocn (affects cg2d residual)
888    o seaice: add runtime flags for turning angles (default to zero)
889    o Adding runtime parameter to exf/, ctrl/, to remove on-the-fly global mean
890      and trend from exf forcing and ctrl control adjustments
891    o fix variable aliasing in gad_calc_rhs that cannot be handled by TAF
892      (since checkpoint57x_post)
893    o change the default rotation period to 86164.s = the Earth rotation
894    o 1rst implementation of Implicit IGW using the 3-D solver (use3Dsolver=T)
895      and based on a reference stratification. Tested within hs94.cs-32x32x5.
896    o seaice advection: add code for choosing between the default (2nd order
897      central differences) and multiDim advection schemes provided by
898      pkg/generic_advdiff
899    o seaice:
900      - removed all references to SEAICE_GRID.h fields from
901        dynsolver, advect, diffus, lsr, without changing the results of lab_sea
902        (cubed-sphere configuration will change a little)
903      - grid computations in seaice_init are obsolete now.
904      - cleaned up code a little so that is easier to read (hopefully).
905      - added new (better?) discretizations of default advection and diffusion
906        (turn on with SEAICEuseFluxForm)
907      - replace 1 in 3d global fields by kSurface in growth.F
908      
909    checkpoint58a_post
910    o seaice:
911      - bug fix in advect.F
912    o shelfice:
913      - separate shelfice load anomaly from pload (breaks with time
914        dependent forcing), => introduce constant field shelficeLoadAnomaly.
915        Its default is 0., but it may be computed more cleverly from (unknown)
916        t- and s-profiles (tRef, sRef) and actual EOS. For now this has to be
917        done offline. A good approximation of the pressure load anomaly is
918        necessary to avoid large initial adjustment processes underneath
919        deep-reaching shelfice.
920      - small fix in ISOMIP shelfice_thermodynamics
921      - add more sophisticated thermodynamics of Hellmer (1989), this is
922        now the default
923      - give a few constants more intuitive names
924    o add code to balance EmPmP and Qnet at the end of do_ocean_physics. Useful
925      if bulk formulae are used in long integration (especially EmPmR). Turn
926      on with balanceEmPmR = .true. or balanceQnet = .true. in data, PARM01
927      if balancePrintMean, the imbalance that is substracted is printed to
928      STDOUT.
929    o fix bug (typo) in obcs_apply_eta.F
930    o add a new package shelfice which enables us to model the circulation
931      underneath shelf-ice with draughts of hundreds of meters.
932     - works
933     - to do: + include improved thermodynamics
934              + check whether kSurfC (from model/inc/SURFACE.h) can be used
935                instead of new field kTopC
936              + can we use topoFile, Ro_surf and existing code in ini_depth.F
937                instead of new field R_shelfIce and new code in ini_depth.F
938                and ini_mask_etc.F?
939              + adjust vertical mixing schemes?
940    o seaice pkg:
941     - add a cpp-flag to include a simple formula for a salinity dependent
942       freezing point of sea water at the surface
943     - change the contents of SEAICE_TEST_ICE_STRESS_1 so that zonal and
944       meridional stresses are now different (and hopefully correct)
945    o AIM pkg: change threshold on large-scale condensation to conserve Heat.
946       update results of aim.5l_LatLon test ; fix title & units of AIM diagnostics
947       and  change 3 diagnostics names (OSR,OSRCLR,KM -> TSR,TSRCLR,DRAG)
948    o pkg/diagnostics: add options and parameters for regional-statistics
949       diagnostics ; define regions by reading a region-mask from a file
950       (might add other options later)
951    o pkg/bulk_force:
952     - add option and parameters to use AIM surface-flux formulae.
953     - Change loading part: S/R BULKF_FIELDS_LOAD only take care of bulkf_fields ;
954       others forcing fields (defined in PARM05, parameter file "data") are loaded
955       from S/R EXTERNAL_FIELDS_LOAD, as usually (with useBulkforce = T or F).
956     - initialise all bulkf_fields in bulkf_init.F ; do in-lining of exf_bulkcdn.F
957     - use the right EXCH call for uwind,vwind (to work on CS-grid).
958     - re-arrange header files (move parameters from BULKF.h to BULKF_PARAMS.h)
959       and parameters (note: calcWindStress replaces .NOT.readwindstress).
960     - cleaner interface with pkg/thSIce (new S/R THSICE_GET_PRECIP).
961    
962    checkpoint58
963    o add "--embed-source" option to genmake2 which, when the supporting
964      tools can be compiled (as determined by genmake2) will turn on the
965      embed_files package which then embeds the entire MITgcm source code
966      (*.[fFhc] + Makefile) used for the build within the executable
967      - requested by CNH but off by default
968      - adds a paltry <9MB to the mitgcmuv executable in most cases
969      - only writes the output when useEMBEDSRC in eedata is true
970    o clean up 3-dim. relaxation codes:
971      * Fix I/O inconsistency in pkg/rbcs: replace precFloat32 by readBinaryPrec
972      * Remove 3-dim. relaxation code from pkg/exf (now use only pkg/rbcs)
973      * Thanks to Tom Haine for testing!
974    
975    checkpoint57z_post
976    o make CG3D solver compatible with Free-surface at k > 1 (p-coordinate):
977      affects output (@ truncation level) of exp. plume_on_slope ; updated.
978    o fix the pickup behavior for obcs in combination with ptracers
979    o fix a bug in ptracers_external_fields_load
980    o no AB-2 at the first iteration for Gw (consistent with Gu,Gv,Gt,Gs ...)
981      affects results of NH experiments (but all our NH tests have Gw[it=1]==0 !!)
982    o transfered surface NH pressure to eta field (if exactConserv).
983    o gmredi: fix bugs in slope tapering ldd97 (depthZ had the wrong sign)
984         and update lab_sea output.txt file.
985    o completing 3-dim. relaxation code: additional term
986         1/tau*( theta(i,j,k) - thetaStar(i,j,k) )
987      in S/R EXTERNAL_FORCING_T (file external_forcing.F)
988      * At compile time, in "EXF_OPTIONS.h" set
989          #define  ALLOW_CLIMTEMP_RELAXATION
990          #define  ALLOW_CLIMSALT_RELAXATION
991      * At runtime in "data", under &PARM03 set (e.g., units in seconds)
992          tauThetaClimRelax3Dim = 15552000.0,
993          tauSaltClimRelax3Dim  = 15552000.0,
994      * 3 cases:
995          1) Use a constant-in-time 3-dim. field
996          2) Provide 12 3-dim. fields corresponding to Jan., ... , Dec.
997          3) Real-time relax. to time-evolving prescribed field
998    o Adding Laplacian-type smoothness constraint on
999      initial and boundary (forcing) controls (ic, bc)
1000      * enable at compile-time via
1001        ALLOW_SMOOTH_IC_COST_CONTRIBUTION, ALLOW_SMOOTH_BC_COST_CONTRIBUTION
1002      * enable at run-time via mult_smooth_ic = 1, mult_smooth_bc = 1
1003      * Absolute scale somewhat unclear so far
1004      * no area weighting was included since no other cost term does so far
1005    
1006    checkpoint57y_post
1007    First step for a NLFS adjoint
1008    o initially suppress rStar (new flag DISABLE_RSTAR_CODE)
1009    o new init. routines for calc_r_star, calc_surf_dr
1010    o still need to deal with ini_masks_etc
1011    o testreport seemed happy
1012    checkpoint57y_pre
1013    
1014    o obcs: always reset wVel & eta (to zero or prescribe it) at the OBs.
1015    o add new package rbcs (for relaxing ptracers at boundaries/depth/surface etc)
1016    o add new offset feature to offline pkg (plus minor cleanup)
1017    o cfc fixes for final year of integration
1018    o clean up GCHEM_OPTIONS.h/DIC_OPTIONS.h (all options should
1019      be in GCHEM_OPTIONS).
1020    
1021    checkpoint57x_post
1022    o fix testreport Pb in multiple test experiment.
1023    o cleanup our namelist syntax in verification:
1024      - make it more F95 standards compliant (some work still needed)
1025      - allows the vast majority of our tests to work with gfortran
1026    o Non-Hydrostatic:
1027     - put all NH variables (formerly in DYNVARS.h & GW.h) in NH_VARS.h
1028     - fix exchange calls for CS-grid using the new EXCH_S3D_RL.
1029    o Allow to apply AB on T,S rather than on AB(gT,gS):
1030     - implemented within #ifdef ALLOW_ADAMSBASHFORTH_3
1031     - use the same arrays (gtNm,gsNm) to hold tracer field at previous
1032       time-steps (if AB(T,S)) and tendencies (if AB(gT,gS)).
1033     - need a "clever" read_pickup to restart from the other AB formulation
1034    o move local commom bloc /GlobalLo/ (used for singleCpuIO) in EESUPPORT.h
1035    o remove some unused variables (reduces number of compiler warnings)
1036    o adjoint
1037      * Disable useVariableViscosity for adjoint for time being
1038        (there are a number of extensive recomputations)
1039      * Initialize certain variables needed for adjoint
1040    
1041    checkpoint57w_post
1042    o pkg/mdsio: use MAX_LEN_FNAM (instead of hard coded 80) for file-names
1043                 fix the singleCpuIO RS version of MDSWRITEFIELD
1044       and add a WARNING if using globalFiles=T with multi-processors.
1045    o write grid-file(s) in only one format (MDS or MNC): default=MNC (if
1046      using MNC); can force MDS output by setting writegrid_mnc=F in data.mnc
1047    o tracer advection scheme:
1048      add DST-2 (=Lax-Wendroff) & 1rst order upwind schemes (the way to get
1049       those 2 schemes before, changing GAD_FLUX_LIMITER.h + to recompile,
1050       was not very convenient).
1051      add implicit version for DST-3 & DST3_Flux_Limit vertical advection;  
1052       (further tests needed for the implicit DST & Flux-Limiter schemes).
1053    o PTRACERS: added namelist parameter PTRACERS_ref in analogy to tRef
1054      and sRef for convenience, handy, when you want to initialize
1055      ptracers in a large domain with a constant non-zero value. Also,
1056      untangle ptracers_init.F a little.
1057    
1058    checkpoint57v_post
1059    o change dome exp. to use variable viscosity in side-drag terms.
1060    o remove all the files from the cfc_offline test since they are now
1061      incorporated into tutorial_cfc_offline which has been producing
1062      identical results for a few days of testing
1063    o add new parameter: sideDragFactor to enable half-slip-side BC
1064      and change side-drag S/R to use viscosity from mom_calc_visc
1065      (can switch back by setting sideDragFactor=0.); affects results at
1066      truncation level; regenerate output for exp.: global_ocean.cs32x10(x3),
1067       global_ocean_ebm, global_ocean_pressure, matrix_example & MLAdjust(x5).
1068    o vorticity & strain are now computed without masking, to account for
1069      no-slip-side BC in variable viscosity calculation ; mask is applied
1070      anyway later on, before computing advection/coriolis terms.
1071    o modify exp4 to test new obcs support for reading from external files
1072      and for passive tracers
1073    o fix behavior of ptracers_monitor when monitor output is written to a
1074      netcdf-file; still not independent of monitor.F (writes in the same
1075      file).
1076    o change default value of tRef (put a uniform, meaningful value for ocean
1077      & atmos) and initialize sRef (was missing, as Martin mentioned).
1078    o Redefine viscC?Leith*.  Change the coefficients of Leith viscosity
1079      to be proportional to enstrophy dissipation length.  Thus,
1080       viscC?leith?_new=pi*(viscC?leith?_old)^(1/3)
1081      This is now consistent with Smagorinsky and with the manual.
1082    
1083    checkpoint57u_post
1084    o OBCS and PTRACERS: add open boundary support for passive tracers
1085      - either use homogenous (pseudo) v.Neumann conditions or prescribe
1086        OB-values from file; this is not different from the way theta and salinity
1087        are treated
1088      - however, Orlanski-radiation conditions are not supported, and the model
1089        will stop if you use pTracers and Orlanski at the same time.
1090      - beefed up the rountine obcs_external_fields_load: now only those open
1091        boundary values are overwritten with values from files for which there
1092        are really files, otherwise the OB-fields remain untouched. This makes
1093        it possible to use different OBs at different ends of the domain (as
1094        with EXF)
1095    o reduce number of exch calls in shap_filt (s2).
1096    o CS-grid: fix divergence contribution to Leith viscosity. Affects (@
1097      truncation level) 4/5 MLAdjust test results (11&12 digits match).
1098    
1099    checkpoint57t_post
1100    o test biharmonic viscosity + no-slip with exp: global_ocean.cs32x15.viscA4
1101    o finish adding brackets (coriolis S/R, vecinv) in multi-terms sum to get
1102      same truncation, independent of the face number: affects affects several
1103      test. exp.: Update global_ocean.cs32x15 (+.thsice) & MLAdjust (all 5).
1104    o fix bug in mom_v_sidedrag (biharmonic viscosity was counted 2 times);
1105      note that biharmonic viscosity + no-slip was not tested in any experiment.
1106    o fix bug in non-linear free-surf side-drag ; generate new output for
1107      global_ocean.cs32x15(+.thsice) & global_ocean_pressure.
1108    o make mnc honor the writeBinaryPrec flag for most kinds of output
1109    o eesupp: split EEPARAMS into EESIZE/EEPARAMS and add a vector global sum
1110    o minor change in averaging W (mom_vi_?_vertshear.F) that affects truncation
1111      error; update output from global_ocean.cs32x15(+.thsice) & MLAdjust (all 5).
1112    o add brackets in multi-terms sum to get same truncation, independent of
1113      the face number (manage to get exactly same value of gU,gV at the cs-edge)
1114      affects several test. exp. Update global_ocean.cs32x15 (+.thsice).
1115    o Clean, new version of mom_calc_visc.  Adds a new feature, viscAhRemax
1116      and viscA4Remax, which allow one to limit the minimum viscosity by specifying
1117      a maximum grid-scale Reynolds number.  Also, changes all length calculations
1118      in the case of grid anisotropy to geometric mean of dx**2 and dy**2.
1119      Suggested values of viscosity parameters found in mom_calc_visc.
1120      Many new viscosity diagnostics available.
1121    
1122    checkpoint57s_post
1123    o Add clearing-house for viscosity calculations, mom_calc_visc and
1124      correct numerous bugs in LeithD and Smagorinsky discretizations.  
1125      mom_calc_visc now allows for Smagorinsky, Leith and LeithD to be
1126      used simultaneously, and to be used in mom_vecinv and mom_fluxform.
1127      Mom_vecinv can be used with standard viscous calculation (mom_vi_hdissip.F)
1128      and with Strain-Tension viscous term calculation (mom_hdissip.F).  
1129      The Strain-Tension form is now called with useStrainTensonVisc=.true.
1130      ViscAhStrain and viscAhTension are now retired.
1131    o diagnostics "VISCAHD" & "VISCA4D" replace "VISCAH" & "VISCA4".
1132    o In response to JMC's bug report, genmake2 now ignores any soft-links
1133      that it finds in the *current* directory when searching for files.
1134      Soft-links found in any other source directories will still work as
1135      they did before.
1136    o add HAVE_SETRLSTK define and useSETRLSTK flag (eedata) which calls
1137      a C routine to unlimit the stack size
1138    o mnc-ify pkg/aim snapshot vars
1139    o mnc-ify pkg/land as requested by Daniel
1140    o various changes to mnc including:
1141      - all files use the new "BASENAME[[.ITER].{t|f}NUM].nc" format
1142      - output can now be grouped so that all files within a group
1143          change the ITER portion of their names in lock-step together
1144      - can now read ("global") PER-FACE (in addition to PER-TILE) files
1145          and works with both EXCH1 and EXCH2 (but needs more testing)
1146      - writing works for all verification test cases w/ g77 on Linux
1147    
1148    checkpoint57r_post
1149    o make MNC variable initialization happen earlier
1150    o add diagnostics for (almost) each term of the momentum Eq.
1151    o remove SST,SSS,UVEL_k2,VVEL_k2 diagnostics.
1152    o move pkg timeave out of pkg-groups "oceanic" & "atmospheric" (pkg/pkg_groups)
1153    o remove MINIMAL_TAVE_OUTPUT option ;
1154      add "dumpInitAndLast" to replace "nodumps" (and MINIMAL_TAVE_OUTPUT).
1155    o move some basic S/R (used elsewhere in the code) from pkg/mdsio to eesupp/src
1156      allows to compile without pkg/mdsio (& test successfully hs94.1x64x5)
1157    o add MNC output for adjoint of EXF (adexf), SEAICE (adseaice)
1158    o add time-dependent SST, SSS control
1159    o cost terms in ecco/ modularized (new cost_generic.F)
1160    o cost_averages routines are modularized (new cost_averagesgeneric.F)
1161    o new infrastructure for seaice model vs. obs misfits in seaice/
1162      * driver from the_main_loop.F is seaice_cost_driver.F
1163      * first term is AREA vs. SMR observation misfit (ALLOW_SEAICE_COST_SMR_AREA)
1164      * gradient check in Exp. 6a of natl_box_adjoint/
1165    o natl_box_adjoint input_seaice for Lab. Sea now available online via wget
1166      (see README file)
1167    
1168    checkpoint57q_post
1169    o fix initialisation Pb in calc_gw (get NANs in exp5 with g77)
1170    o fix annoying months-old bug in mnc/mdsio output for seaice pkg
1171      - bug was reported by Jean-Michel and Ian Fenty
1172    o fix initialization Pb in AIM-Ocean coupled model (aim_sice2aim.F)
1173      update exp. cpl_aim+ocn output.
1174    o Implement 4-level checkpointing: AUTODIFF_4_LEVEL_CHECKPOINT
1175      Needed for high-res. runs with large global files
1176      to be able to limit tapelev size
1177    o Changed some tests for adjoint:
1178      * carbon/ now tests AUTODIFF_2_LEVEL_CHECKPOINT
1179      * natl_box_adjoint/code_bulk/ tests AUTODIFF_4_LEVEL_CHECKPOINT
1180      * global_ocean.90x40x15/ back to default 3-level checkpointing
1181    o Modifications to enable scripted COMMON to MODULE conversion
1182      * verification/OpenAD/code/ has necessary scripts and description;
1183      * converts, compiles and runs successfully;
1184    
1185    checkpoint57p_post
1186    o reading of delXfile & delYfile moved from ini_parms.F to ini_grid.F
1187    o move ${PKG}_MNC_INIT from ${PKG}_READ_PARAMS to ${PKG}_INIT_FIXED
1188      (already the case for some pkgs, including recent MNC_init, e.g. thsice)
1189    o call CALC_GW from DYNAMICS (instead of from FORWARD_STEP)
1190    o Dissipation & phiHyd gradient are always added to gU,gV in timestep.F
1191      (was already the case for dissipation with mom_vecinv,
1192       and also the case for grad.PhiHyd when staggered-timeStep)
1193      This will allow to put dissipation out-off the AB time-stepping.
1194     Unfortunately, affects truncation error. Update output of exp. that "fails"
1195      (cg2d matching number) and leave the others for later: front_relax(10),
1196      global_ocean_pressure(10),ideal_2D_oce(10),internal_wave(9),lab_sea(12),
1197      matrix_example(7!),natl_box(12),plume_on_slope(11),vermix(12x3,11x2).
1198    
1199    checkpoint57o_post
1200    o fix MNC/MDSIO flags in PTRACERS so that (1) it works, and
1201      (2) its ready to be documented during the 20050801 DocFest
1202    o MNC-ify the gmredi package -- tested and works w/ and w/o mnc
1203      for ideal_2D_oce and lab_sea on linux_ia32_g77
1204    o set to #undef CTRL_SET_OLD_MAXCVARS_30
1205      in global1x1_tot/code_seaice_adj to access indices 32, 33
1206      (worth another tag)
1207    
1208    checkpoint57n_post
1209    o adding precip control xx_precip 32
1210    o adding swflux control xx_swflux 33
1211    o Replacing 10 forcing penalty cost routines by 1 generic.
1212    o Implementing partitioning in time-mean and variable adjustment
1213      for atmos. state.
1214    o Time-mean constant error is now read in data.ecco (instead of hard-coded)
1215  o in natl_box_adjoint:  o in natl_box_adjoint:
1216    * updated: results_bulk/    * updated exp 1 to 10
1217    * not yet updated: results/, results_seaice/      (but does not have time-mean vs. variable split results yet)
1218    o updated global1x1/*_seaice_adj/
1219      to incorporate latest changes
1220    o enable useSingleCpuIO for mdsio vector routines
1221      (applies in particular to tapelev I/O)
1222    o removed inefficient K-loop in all active_file*control*.F
1223    
1224  checkpoint57m_post  checkpoint57m_post
1225  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)  o re-arrange exp. adjustment.cs-32x32x1 (adjust_nlfs.cs-32x32x1 merge into)
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